Analysis pipeline for human LINE-1 targeted sequencing data obtained with the SLAV-Seq protocol.
https://doi.org/10.1038/nn.4388
- rf
- pyslavseq
- snakemake
- cutadapt
- bwa-mem
- tabix
- python
- perl
This pipeline uses rf (https://github.com/apuapaquola/rf) to manage workflow.
- clone the repository
- move the pipeline directory to a suitable location
- edit _h/run scripts or set the BASE_DIR to /path/to/pipeline
- go to pipeline/genome and
rf run -r .to download and index hg19 - add your fastq files
- go to pipeline/genome and
rf run -r .